I’d lean towards the subjunctive form of the two verbs, myself, since the expression “ce n’est pas que” can introduce a possibility:

It’s not that someone {might have done / possibly did} something, but rather that …

If the phrase “ce n’est pas que” were followed by “mais c’est que”, I’d use the indicative form in the “c’est que” clause, as it deals with an (established) fact this time:

Ce n’est pas que Pierre Gringoire craignît {subjunctive} monsieur le cardinal ou le dédaignât {subjunctive} , mais (c’est) que … {indicative} …